Dual-specificity RNA methyltransferase RlmN - Escherichia coli (strain B / BL21-DE3)

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C6EKJ2 (C6EKJ2_ECOBD) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 32. History...

Clusters with 100%, 90%, 50% identity |

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info Customize order

Names and origin

Protein names

Recommended name:
Dual-specificity RNA methyltransferase RlmN HAMAP-Rule MF_01849
EC=2.1.1.- HAMAP-Rule MF_01849
EC=2.1.1.192 HAMAP-Rule MF_01849

Alternative name(s):
23S rRNA (adenine(2503)-C(2))-methyltransferase HAMAP-Rule MF_01849
23S rRNA m2A2503 methyltransferase HAMAP-Rule MF_01849
Ribosomal RNA large subunit methyltransferase N HAMAP-Rule MF_01849
tRNA (adenine(37)-C(2))-methyltransferase HAMAP-Rule MF_01849
tRNA m2A37 methyltransferase HAMAP-Rule MF_01849

Gene names

Name:	yfgB EMBL ACT44229.1
Synonyms:	rlmN HAMAP-Rule MF_01849 EMBL CAQ32888.1
Ordered Locus Names:	B21_02371, ECBD_1169, ECD_02409

Organism

Escherichia coli (strain B / BL21-DE3) [Complete proteome] [HAMAP]

Taxonomic identifier

469008 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	384 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity By similarity. HAMAP-Rule MF_01849
Catalytic activity	2 S-adenosyl-L-methionine + adenine(2503) in 23S rRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(2503) in 23S rRNA. HAMAP-Rule MF_01849 SAAS SAAS004383 2 S-adenosyl-L-methionine + adenine₃₇ in tRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine₃₇ in tRNA. HAMAP-Rule MF_01849
Cofactor	Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine By similarity. HAMAP-Rule MF_01849 SAAS SAAS004383
Subcellular location	Cytoplasm By similarity HAMAP-Rule MF_01849 SAAS SAAS004383.
Miscellaneous	Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue By similarity. HAMAP-Rule MF_01849
Sequence similarities	Belongs to the radical SAM superfamily. RlmN family. HAMAP-Rule MF_01849

Ontologies

Keywords
Biological process	rRNA processing HAMAP-Rule MF_01849 SAAS SAAS004383 tRNA processing HAMAP-Rule MF_01849 SAAS SAAS004383
Cellular component	Cytoplasm HAMAP-Rule MF_01849 SAAS SAAS004383
Ligand	4Fe-4S HAMAP-Rule MF_01849 SAAS SAAS004383 Iron Iron-sulfur Metal-binding S-adenosyl-L-methionine HAMAP-Rule MF_01849 SAAS SAAS004383
Molecular function	Methyltransferase HAMAP-Rule MF_01849 SAAS SAAS004383 EMBL CAQ32888.1 Transferase
PTM	Disulfide bond HAMAP-Rule MF_01849 SAAS SAAS004383
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	rRNA base methylation Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: HAMAP metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW rRNA (adenine-C2-)-methyltransferase activity Inferred from electronic annotation. Source: HAMAP rRNA binding Inferred from electronic annotation. Source: HAMAP tRNA (adenine-C2-)-methyltransferase activity Inferred from electronic annotation. Source: HAMAP tRNA binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Regions

Region

179 – 180

S-adenosyl-L-methionine binding By similarity HAMAP-Rule MF_01849

Region

233 – 235

S-adenosyl-L-methionine binding By similarity HAMAP-Rule MF_01849

Sites

Active site

105

Proton acceptor By similarity HAMAP-Rule MF_01849

Active site

355

S-methylcysteine intermediate By similarity HAMAP-Rule MF_01849

Metal binding

125

Iron-sulfur (4Fe-4S-S-AdoMet) By similarity HAMAP-Rule MF_01849

Metal binding

129

Iron-sulfur (4Fe-4S-S-AdoMet) By similarity HAMAP-Rule MF_01849

Metal binding

132

Iron-sulfur (4Fe-4S-S-AdoMet) By similarity HAMAP-Rule MF_01849

Binding site

211

S-adenosyl-L-methionine By similarity HAMAP-Rule MF_01849

Binding site

312

S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen By similarity HAMAP-Rule MF_01849

Amino acid modifications

Disulfide bond

118 ↔ 355

(transient) By similarity HAMAP-Rule MF_01849

Sequences

Sequence

Length

Mass (Da)

Tools

C6EKJ2 [UniParc].

Last modified September 1, 2009. Version 1.
Checksum: 92C1BDCC840FCE7B
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FASTA

384

43,086

        10         20         30         40         50         60 
MSEQLVTPEN VTTKDGKINL LDLNRQQMRE FFKDLGEKPF RADQVMKWMY HYCCDNFDEM 

        70         80         90        100        110        120 
TDINKVLRGK LKEVAEIRAP EVVEEQRSSD GTIKWAIAVG DQRVETVYIP EDDRATLCVS 

       130        140        150        160        170        180 
SQVGCALECK FCSTAQQGFN RNLRVSEIIG QVWRAAKIVG AAKVTGQRPI TNVVMMGMGE 

       190        200        210        220        230        240 
PLLNLNNVVP AMEIMLDDFG FGLSKRRVTL STSGVVPALD KLGDMIDVAL AISLHAPNDE 

       250        260        270        280        290        300 
IRDEIVPINK KYNIETFLAA VRRYLEKSNA NQGRVTIEYV MLDHVNDGTE HAHQLAELLK 

       310        320        330        340        350        360 
DTPCKINLIP WNPFPGAPYG RSSNSRIDRF SKVLMSYGFT TIVRKTRGDD IDAACGQLAG 

       370        380 
DVIDRTKRTL RKRMQGEAID IKAV

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References

[1]	"Genome sequences of Escherichia coli B strains REL606 and BL21(DE3)." Jeong H., Barbe V., Lee C.H., Vallenet D., Yu D.S., Choi S.H., Couloux A., Lee S.W., Yoon S.H., Cattolico L., Hur C.G., Park H.S., Segurens B., Kim S.C., Oh T.K., Lenski R.E., Studier F.W., Daegelen P., Kim J.F. J. Mol. Biol. 394:644-652(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: B / BL21-DE3 [Korea].
[2]	"Sequencing and gene expression analysis of Escherichia coli BL21." Leparc G., Striedner G., Bayer K., Kreil D., Krempl P.M. Submitted (JUN-2009) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: B / BL21-DE3 [Austria].
[3]	"Complete sequence of Escherichia coli BL21(DE3)." Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., LaButti K.M., Clum A., Larimer F., Land M., Hauser L., Kyrpides N., Anderson I., Sorek R., Rubin E. Submitted (JUL-2009) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: B / BL21-DE3 [JGI].

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001665 Genomic DNA. Translation: ACT28235.1. CP001509 Genomic DNA. Translation: ACT44229.1. AM946981 Genomic DNA. Translation: CAQ32888.1.
RefSeq	YP_003000146.1. NC_012892.2. YP_003035420.1. NC_012947.1. YP_003055000.1. NC_012971.2.
3D structure databases
SMR	C6EKJ2. Positions 17-349.
ModBase	Search...
Protein-protein interaction databases
STRING	469008.ECBD_1169.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ACT28235; ACT28235; ECBD_1169. ACT44229; ACT44229; ECD_02409. CAQ32888; CAQ32888; B21_02371.
GeneID	8114144. 8156832. 8181113.
KEGG	ebd:ECBD_1169. ebe:B21_02371. ebl:ECD_02409.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0820.
HOGENOM	HOG000217992.
KO	K06941.
OMA	IYHFGVS.
ProtClustDB	PRK11194.
Family and domain databases
Gene3D	3.20.20.70. 1 hit.
HAMAP	MF_01849. 23SrRNA_methyltr_N.
InterPro	IPR013785. Aldolase_TIM. IPR006638. Elp3/MiaB/NifB. IPR004383. rRNA_lsu_MTrfase_RlmN. IPR007197. rSAM. [Graphical view]
Pfam	PF04055. Radical_SAM. 1 hit. [Graphical view]
PIRSF	PIRSF006004. CHP00048. 1 hit.
SMART	SM00729. Elp3. 1 hit. [Graphical view]
TIGRFAMs	TIGR00048. TIGR00048. 1 hit.
ProtoNet	Search...

Entry information

Entry name

C6EKJ2_ECOBD

Accession

Primary (citable) accession number: C6EKJ2
Secondary accession number(s): C5W7L9

Entry history

Integrated into UniProtKB/TrEMBL:	September 1, 2009
Last sequence update:	September 1, 2009
Last modified:	May 1, 2013
This is version 32 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Regions

Sites

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information